1
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Zubčić K, Franić D, Pravica M, Hof PR, Šimić G, Boban M. Effects of heterologous human tau protein expression in yeast models of proteotoxic stress response. CNS Neurosci Ther 2024; 30:e14304. [PMID: 37341072 PMCID: PMC11163194 DOI: 10.1111/cns.14304] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND The primary histological characteristic of Alzheimer's disease is the presence of neurofibrillary tangles, which are large aggregates of tau protein. Aging is the primary risk factor for the development of Alzheimer's disease, however, the underlying causes of tau protein aggregation and toxicity are unclear. AIMS Here we investigated tau aggregation and toxicity under the conditions of compromised protein homeostasis. METHODS We used heterologous expression of human tau protein in the unicellular eukaryote yeast Saccharomyces cerevisiae with evolutionarily conserved protein quality control pathways and examined tau-dependent toxicity and aggregation using growth assays, fluorescence microscopy, and a split luciferase-based reporter NanoBiT. RESULTS Tau protein expressed in yeast under mild proteotoxic stress, or in mutants with impaired pathways for proteotoxic stress response, did not lead to synthetic toxicity or the formation of obvious aggregates. Chronologically old cells also did not develop observable tau aggregates. Our examination of tau oligomerization in living cells using NanoBiT reporter suggests that tau does not form significant levels of oligomers under basal conditions or under mild proteotoxic stress. CONCLUSION Together our data suggest that human tau protein does not represent a major burden to the protein quality control system in yeast cells.
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Affiliation(s)
- Klara Zubčić
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
| | - Dina Franić
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
| | - Mihaela Pravica
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's DiseaseFriedman Brain Institute, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Goran Šimić
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
| | - Mirta Boban
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
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2
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Wang Y, Song X, Wang Y, Wang N. Specific interaction of insulin receptor and GLP-1 receptor mediates crosstalk between their signaling. Biochem Biophys Res Commun 2022; 636:31-39. [DOI: 10.1016/j.bbrc.2022.10.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 11/02/2022]
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3
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O'Neill S, Knaus UG. Bioluminescence-Based Complementation Assay to Correlate Conformational Changes in Membrane-Bound Complexes with Enzymatic Function. Methods Mol Biol 2022; 2525:123-137. [PMID: 35836064 DOI: 10.1007/978-1-0716-2473-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The proteomics field has undergone tremendous development with the introduction of many innovative methods for the identification and characterization of protein-protein interactions (PPIs). Sensitive and quantitative protein association-based techniques represent a versatile tool to probe the architecture of receptor complexes and receptor-ligand interactions and expand the drug discovery toolbox by facilitating high-throughput screening (HTS) approaches. These novel methodologies will be highly enabling for interrogation of structural determinants required for the activity of multimeric membrane-bound enzymes with unresolved crystal structure and for HTS assay development focused on unique characteristics of complex assembly instead of common catalytic features, thereby increasing specificity. We describe here an example of a binary luciferase reporter assay (NanoBiT®) to quantitatively assess the heterodimerization of the catalytically active NADPH oxidase 4 (NOX4) enzyme complex. The catalytic subunit NOX4 requires association with the protein p22phox for stabilization and enzymatic activity, but the precise manner by which these two membrane-bound proteins interact to facilitate hydrogen peroxide (H2O2) generation is currently unknown. The NanoBiT complementation reporter quantitatively determined the accurate, reduced, or failed complex assembly, which can then be confirmed by determining H2O2 release, protein expression, and heterodimer trafficking. Multimeric complex formation differs between NOX enzyme isoforms, facilitating isoform-specific, PPI-based drug screening in the future.
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Affiliation(s)
- Sharon O'Neill
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
- Legend Biotech, Dublin, Ireland
| | - Ulla G Knaus
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland.
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4
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Listunov D, Linhares BM, Kim E, Winkler A, Simes ML, Weaver S, Cho HJ, Rizo A, Zolov S, Keshamouni VG, Grembecka J, Cierpicki T. Development of potent dimeric inhibitors of GAS41 YEATS domain. Cell Chem Biol 2021; 28:1716-1727.e6. [PMID: 34289376 DOI: 10.1016/j.chembiol.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022]
Abstract
GAS41 is an emerging oncogene overexpressed and implicated in multiple cancers, including non-small cell lung cancer (NSCLC). GAS41 is a dimeric protein that contains the YEATS domain, which is involved in the recognition of lysine-acylated histones. Here, we report the development of GAS41 YEATS inhibitors by employing a fragment-based screening approach. These inhibitors bind to GAS41 YEATS domain in a channel constituting a recognition site for acylated lysine on histone proteins. To enhance inhibitory activity, we developed a dimeric analog with nanomolar activity that blocks interactions of GAS41 with acetylated histone H3. Our lead compound engages GAS41 in cells, blocks proliferation of NSCLC cells, and modulates expression of GAS41-dependent genes, validating on-target mechanism of action. This study demonstrates that disruption of GAS41 protein-protein interactions may represent an attractive approach to target lung cancer cells. This work exemplifies the use of bivalent inhibitors as a general strategy to block challenging protein-protein interactions.
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Affiliation(s)
- Dymytrii Listunov
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Brian M Linhares
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - EunGi Kim
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Alyssa Winkler
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Miranda L Simes
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Sidney Weaver
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Hyo Je Cho
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Alexandrea Rizo
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Sergey Zolov
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2670, USA
| | - Venkateshwar G Keshamouni
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2670, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA.
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA.
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5
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Yurugi H, Zhuang Y, Siddiqui FA, Liang H, Rosigkeit S, Zeng Y, Abou-Hamdan H, Bockamp E, Zhou Y, Abankwa D, Zhao W, Désaubry L, Rajalingam K. A subset of flavaglines inhibits KRAS nanoclustering and activation. J Cell Sci 2020; 133:jcs244111. [PMID: 32501281 DOI: 10.1242/jcs.244111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/30/2020] [Indexed: 08/31/2023] Open
Abstract
The RAS oncogenes are frequently mutated in human cancers and among the three isoforms (KRAS, HRAS and NRAS), KRAS is the most frequently mutated oncogene. Here, we demonstrate that a subset of flavaglines, a class of natural anti-tumour drugs and chemical ligands of prohibitins, inhibit RAS GTP loading and oncogene activation in cells at nanomolar concentrations. Treatment with rocaglamide, the first discovered flavagline, inhibited the nanoclustering of KRAS, but not HRAS and NRAS, at specific phospholipid-enriched plasma membrane domains. We further demonstrate that plasma membrane-associated prohibitins directly interact with KRAS, phosphatidylserine and phosphatidic acid, and these interactions are disrupted by rocaglamide but not by the structurally related flavagline FL1. Depletion of prohibitin-1 phenocopied the rocaglamide-mediated effects on KRAS activation and stability. We also demonstrate that flavaglines inhibit the oncogenic growth of KRAS-mutated cells and that treatment with rocaglamide reduces non-small-cell lung carcinoma (NSCLC) tumour nodules in autochthonous KRAS-driven mouse models without severe side effects. Our data suggest that it will be promising to further develop flavagline derivatives as specific KRAS inhibitors for clinical applications.
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Affiliation(s)
- Hajime Yurugi
- Cell Biology Unit, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
| | - Yinyin Zhuang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637457 Singapore
| | - Farid A Siddiqui
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, Mcgovern Medical School, UT Health, 6431 Fannin St. MSE R382, Houston, TX 77030, USA
| | - Sebastian Rosigkeit
- Cell Biology Unit, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
| | - Yongpeng Zeng
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637457 Singapore
| | - Hussein Abou-Hamdan
- Therapeutic Laboratory of Cardio-Oncology and Medicinal Chemistry (FRE 2033), CNRS, University of Strasbourg, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg, France
| | - Ernesto Bockamp
- Institute for Translational Immunology and Research Center for Immunotherapy, University Medical Center, Johannes Gutenberg University, D 55131 Mainz, Germany
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, Mcgovern Medical School, UT Health, 6431 Fannin St. MSE R382, Houston, TX 77030, USA
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
- Cancer Cell Biology and Drug Discovery Group, Life Sciences Research Unit University of Luxembourg, L 4362 Esch-sur-Alzette, Luxembourg
| | - Wenting Zhao
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637457 Singapore
| | - Laurent Désaubry
- Therapeutic Laboratory of Cardio-Oncology and Medicinal Chemistry (FRE 2033), CNRS, University of Strasbourg, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg, France
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
- University Cancer Center Mainz, University Medical Center Mainz, D 55131 Mainz, Germany
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6
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Hinkley TC, Garing S, Jain P, Williford J, Le Ny ALM, Nichols KP, Peters JE, Talbert JN, Nugen SR. A Syringe-Based Biosensor to Rapidly Detect Low Levels of Escherichia Coli (ECOR13) in Drinking Water Using Engineered Bacteriophages. SENSORS (BASEL, SWITZERLAND) 2020; 20:E1953. [PMID: 32244369 PMCID: PMC7181147 DOI: 10.3390/s20071953] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023]
Abstract
A sanitized drinking water supply is an unconditional requirement for public health and the overall prosperity of humanity. Potential microbial and chemical contaminants of drinking water have been identified by a joint effort between the World Health Organization (WHO) and the United Nations Children's Fund (UNICEF), who together establish guidelines that define, in part, that the presence of Escherichia coli (E. coli) in drinking water is an indication of inadequate sanitation and a significant health risk. As E. coli is a nearly ubiquitous resident of mammalian gastrointestinal tracts, no detectable counts in 100 mL of drinking water is the standard used worldwide as an indicator of sanitation. The currently accepted EPA method relies on filtration, followed by growth on selective media, and requires 24-48 h from sample to results. In response, we developed a rapid bacteriophage-based detection assay with detection limit capabilities comparable to traditional methods in less than a quarter of the time. We coupled membrane filtration with selective enrichment using genetically engineered bacteriophages to identify less than 20 colony forming units (CFU) E. coli in 100 mL drinking water within 5 h. The combination of membrane filtration with phage infection produced a novel assay that demonstrated a rapid, selective, and sensitive detection of an indicator organism in large volumes of drinking water as recommended by the leading world regulatory authorities.
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Affiliation(s)
- Troy C. Hinkley
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Spencer Garing
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Paras Jain
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - John Williford
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Anne-Laure M. Le Ny
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Kevin P. Nichols
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Joseph E. Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA;
| | - Joey N. Talbert
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA;
| | - Sam R. Nugen
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
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7
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Song X, Yu Y, Shen C, Wang Y, Wang N. Dimerization/oligomerization of the extracellular domain of the GLP-1 receptor and the negative cooperativity in its ligand binding revealed by the improved NanoBiT. FASEB J 2020; 34:4348-4368. [PMID: 31970836 DOI: 10.1096/fj.201902007r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/15/2019] [Accepted: 01/12/2020] [Indexed: 12/13/2022]
Abstract
The glucagon-like peptide-1 receptor (GLP-1R), a family B G-protein coupled receptor (GPCR), regulates the insulin secretion following stimulation by ligands. The transmembrane domain (TM) mediates GLP-1R homodimerization, which modulates its ligand binding and signaling. We investigated the possible involvement of the N-terminal extracellular domain (NTD) in dimerization/oligomerization and dimer-associated ligand binding by NanoLuc Binary Technology (NanoBiT). With improved NanoBiT detection using a decreasing substrate concentration, the negative cooperativity of ligand binding to the NTD was confirmed by accelerated dissociation and Scatchard analysis. The dimerization/oligomerization of the isolated NTD was observed by NanoBiT and validated by analytical ultracentrifugation, deriving the comparable dimerization affinity (~105 M-1 ). The NTD was also involved in the dimerization/oligomerization of the full-length GLP-1R with mutated TM4 at the cellular level. In an analysis of the parameters of the NTD binding, the Kd for the probe GLP-1 (7-36, A8G) was similar (6-8 μM) in both the 1:1 binding model and the receptor dimerization model. Compared with GLP-1 and dulaglutide, exenatide showed two-site binding with Ki values of 1.4 pM and 8.7 nM. Our study indicates the involvement of NTD in the GLP-1R dimerization/oligomerization and suggests that further investigations on the role in other family B GPCRs are needed.
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Affiliation(s)
- Xiaohan Song
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Yi Yu
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Cangjie Shen
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Yubo Wang
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Nan Wang
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
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8
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Elucidation of the Molecular Characteristics of Wild-Type and ALS-Linked Mutant SOD1 Using the NanoLuc Complementation Reporter System. Appl Biochem Biotechnol 2019; 190:674-685. [PMID: 31422561 DOI: 10.1007/s12010-019-03114-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/18/2019] [Indexed: 12/14/2022]
Abstract
Previously, we evaluated human SOD1 (hSOD1) dimerization in living cells using the NanoLuc complementation reporter system and found that homodimerization of G85R and G93A mutant SOD1 was lower than that of wild-type hSOD1. Since these assays were performed only using N-terminal NanoBiT-tagged hSOD1 constructs in our previous study, we constructed additional hSOD1 genes with NanoBiT-tags at the C-terminus and evaluated the NanoBiT luciferase activities. Among the tested combinations, the luciferase activity in cells expressing NanoBiT-tagged wild-type hSOD1 was higher than that in cells expressing G85R or G93A mutant hSOD1. The NanoBiT luciferase activities were detected both inside and outside of cells; however, the extracellular luciferase activities were minimally dampened by treatment with brefeldin A, which inhibits canonical ER-Golgi transport. In addition to studies on the homodimerization of SOD1, we investigated the interaction between hSOD1 and three chaperone proteins, copper chaperone for SOD1 (CCS), FKBP, and GRP78. The NanoBiT luciferase activities in cells expressing NanoBiT-tagged SOD1 and CCS were relatively high, but weak signals were also observed in cells expressing SOD1 together with FKBP or GRP78. These luciferase activities were different between wild-type and mutant hSOD1. Finally, we investigated the effects of two selenocompounds, ebselen and Se-methylselenocysteine, on SOD1 dimerization and found that ebselen increased the NanoBiT luciferase activity in cells expressing wild-type and mutant hSOD1. In conclusion, we show the differential molecular characteristics of wild-type and mutant hSOD1 in live cells by transfection with NanoBiT-tagged hSOD1 and chaperone genes and demonstrate that this assay might be useful for the development and re-evaluation of chemical compounds modulating the SOD1 conformation.
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9
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Luminescence- and Fluorescence-Based Complementation Assays to Screen for GPCR Oligomerization: Current State of the Art. Int J Mol Sci 2019; 20:ijms20122958. [PMID: 31213021 PMCID: PMC6627893 DOI: 10.3390/ijms20122958] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/05/2019] [Accepted: 06/12/2019] [Indexed: 01/22/2023] Open
Abstract
G protein-coupled receptors (GPCRs) have the propensity to form homo- and heterodimers. Dysfunction of these dimers has been associated with multiple diseases, e.g., pre-eclampsia, schizophrenia, and depression, among others. Over the past two decades, considerable efforts have been made towards the development of screening assays for studying these GPCR dimer complexes in living cells. As a first step, a robust in vitro assay in an overexpression system is essential to identify and characterize specific GPCR–GPCR interactions, followed by methodologies to demonstrate association at endogenous levels and eventually in vivo. This review focuses on protein complementation assays (PCAs) which have been utilized to study GPCR oligomerization. These approaches are typically fluorescence- and luminescence-based, making identification and localization of protein–protein interactions feasible. The GPCRs of interest are fused to complementary fluorescent or luminescent fragments that, upon GPCR di- or oligomerization, may reconstitute to a functional reporter, of which the activity can be measured. Various protein complementation assays have the disadvantage that the interaction between the reconstituted split fragments is irreversible, which can lead to false positive read-outs. Reversible systems offer several advantages, as they do not only allow to follow the kinetics of GPCR–GPCR interactions, but also allow evaluation of receptor complex modulation by ligands (either agonists or antagonists). Protein complementation assays may be used for high throughput screenings as well, which is highly relevant given the growing interest and effort to identify small molecule drugs that could potentially target disease-relevant dimers. In addition to providing an overview on how PCAs have allowed to gain better insights into GPCR–GPCR interactions, this review also aims at providing practical guidance on how to perform PCA-based assays.
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10
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Dale NC, Johnstone EKM, White CW, Pfleger KDG. NanoBRET: The Bright Future of Proximity-Based Assays. Front Bioeng Biotechnol 2019; 7:56. [PMID: 30972335 PMCID: PMC6443706 DOI: 10.3389/fbioe.2019.00056] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/04/2019] [Indexed: 12/17/2022] Open
Abstract
Bioluminescence resonance energy transfer (BRET) is a biophysical technique used to monitor proximity within live cells. BRET exploits the naturally occurring phenomenon of dipole-dipole energy transfer from a donor enzyme (luciferase) to an acceptor fluorophore following enzyme-mediated oxidation of a substrate. This results in production of a quantifiable signal that denotes proximity between proteins and/or molecules tagged with complementary luciferase and fluorophore partners. BRET assays have been used to observe an array of biological functions including ligand binding, intracellular signaling, receptor-receptor proximity, and receptor trafficking, however, BRET assays can theoretically be used to monitor the proximity of any protein or molecule for which appropriate fusion constructs and/or fluorophore conjugates can be produced. Over the years, new luciferases and approaches have been developed that have increased the potential applications for BRET assays. In particular, the development of the small, bright and stable Nanoluciferase (NanoLuc; Nluc) and its use in NanoBRET has vastly broadened the potential applications of BRET assays. These advances have exciting potential to produce new experimental methods to monitor protein-protein interactions (PPIs), protein-ligand interactions, and/or molecular proximity. In addition to NanoBRET, Nluc has also been exploited to produce NanoBiT technology, which further broadens the scope of BRET to monitor biological function when NanoBiT is combined with an acceptor. BRET has proved to be a powerful tool for monitoring proximity and interaction, and these recent advances further strengthen its utility for a range of applications.
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Affiliation(s)
- Natasha C Dale
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia.,Australian Research Council Centre for Personalised Therapeutics TechnologiesAustralia
| | - Elizabeth K M Johnstone
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia.,Australian Research Council Centre for Personalised Therapeutics TechnologiesAustralia
| | - Carl W White
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia.,Australian Research Council Centre for Personalised Therapeutics TechnologiesAustralia
| | - Kevin D G Pfleger
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia.,Australian Research Council Centre for Personalised Therapeutics TechnologiesAustralia.,Dimerix Limited, Nedlands, WA, Australia
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11
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Abstract
The stabilization and activation of NOX4 through its binding with p22phox are well documented; however little is known of the precise manner by which these two proteins interact. In recent years, the field of proteomics has undergone tremendous development with the introduction of many novel methods for the identification and characterization of protein-protein interactions (PPIs). To enhance our understanding of structural determinants leading to the association between NOX4 and p22phox, we developed a binary luciferase reporter assay (NanoBiT®) to quantitatively assess NOX4-p22phox heterodimerization. The complementation reporter quantitatively determines the accurate, reduced, or failed complex assembly, which can be confirmed and further interrogated by analyzing NOX4 catalytic activity (H2O2 release), protein expression, and dimer localization. This association-based PPI technique represents both a much-needed expansion of the NOX4 lead discovery tool box and a versatile method to probe the architecture of NOX and DUOX complexes in the future.
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12
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Grañe-Boladeras N, Williams D, Tarmakova Z, Stevanovic K, Villani LA, Mehrabi P, Siu KWM, Pastor-Anglada M, Coe IR. Oligomerization of equilibrative nucleoside transporters: a novel regulatory and functional mechanism involving PKC and PP1. FASEB J 2018; 33:3841-3850. [PMID: 30521377 DOI: 10.1096/fj.201800440rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Equilibrative nucleoside transporters (ENTs) translocate nucleosides and nucleobases across plasma membranes, as well as a variety of anti-cancer, -viral, and -parasite nucleoside analogs. They are also key members of the purinome complex and regulate the protective and anti-inflammatory effects of adenosine. Despite their important role, little is known about the mechanisms involved in their regulation. We conducted membrane yeast 2-hybrid and coimmunoprecipitation studies and identified, for the first time to our knowledge, the existence of protein-protein interactions between human ENT1 and ENT2 (hENT1 and hENT2) proteins in human cells and the formation of hetero- and homo-oligomers at the plasma membrane and the submembrane region. The use of NanoLuc Binary Technology allowed us to analyze changes in the oligomeric status of hENT1 and hENT2 and how they rapidly modify the uptake profile for nucleosides and nucleobases and allow cells to respond promptly to external signals or changes in the extracellular environment. These changes in hENTs oligomerization are triggered by PKC activation and subsequent action of protein phosphatase 1.-Grañe-Boladeras, N., Williams, D., Tarmakova, Z., Stevanovic, K., Villani, L. A., Mehrabi, P., Siu, K. W. M., Pastor-Anglada, M., Coe, I. R. Oligomerization of equilibrative nucleoside transporters: a novel regulatory and functional mechanism involving PKC and PP1.
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Affiliation(s)
- Natalia Grañe-Boladeras
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada.,Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine, University of Barcelona, Barcelona, Spain.,National Biomedical Research Institute of Liver and Gastrointestinal Diseases, Barcelona, Spain
| | - Declan Williams
- Department of Chemistry, York University, Toronto, Ontario, Canada; and
| | - Zlatina Tarmakova
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Katarina Stevanovic
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Linda A Villani
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Pedram Mehrabi
- Department of Biology, York University, Toronto, Ontario, Canada
| | - K W Michael Siu
- Department of Chemistry, York University, Toronto, Ontario, Canada; and
| | - Marçal Pastor-Anglada
- Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine, University of Barcelona, Barcelona, Spain.,National Biomedical Research Institute of Liver and Gastrointestinal Diseases, Barcelona, Spain
| | - Imogen R Coe
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
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13
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Cho HJ, Li H, Linhares BM, Kim E, Ndoj J, Miao H, Grembecka J, Cierpicki T. GAS41 Recognizes Diacetylated Histone H3 through a Bivalent Binding Mode. ACS Chem Biol 2018; 13:2739-2746. [PMID: 30071723 DOI: 10.1021/acschembio.8b00674] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
GAS41 is a chromatin-associated protein that belongs to the YEATS family and is involved in the recognition of acetyl-lysine in histone proteins. A unique feature of GAS41 is the presence of a C-terminal coiled-coil domain, which is responsible for protein dimerization. Here, we characterized the specificity of the GAS41 YEATS domain and found that it preferentially binds to acetylated H3K18 and H3K27 peptides. Interestingly, we found that full-length, dimeric GAS41 binds to diacetylated H3 peptides with an enhanced affinity when compared to those for monoacetylated peptides, through a bivalent binding mode. We determined the crystal structure of the GAS41 YEATS domain with H3K23acK27ac to visualize the molecular basis of diacetylated histone binding. Our results suggest a unique binding mode in which full-length GAS41 is a reader of diacetylated histones.
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Affiliation(s)
- Hyo Je Cho
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hao Li
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brian M. Linhares
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - EunGi Kim
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Juliano Ndoj
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hongzhi Miao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
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14
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Novel Protein Kinase Inhibitors Related to Tau Pathology Modulate Tau Protein-Self Interaction Using a Luciferase Complementation Assay. Molecules 2018; 23:molecules23092335. [PMID: 30213139 PMCID: PMC6225193 DOI: 10.3390/molecules23092335] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/06/2018] [Accepted: 09/08/2018] [Indexed: 02/03/2023] Open
Abstract
The current number of drugs available for the treatment of Alzheimer’s disease (AD) is strongly limited and their benefit for therapy is given only in the early state of the disease. An effective therapy should affect those processes which mainly contribute to the neuronal decay. There have been many approaches for a reduction of toxic Aβ peptides which mostly failed to halt cognitive deterioration in patients. The formation of neurofibrillary tangles (NFT) and its precursor tau oligomers have been suggested as main cause of neuronal degeneration because of a direct correlation of their density to the degree of dementia. Reducing of tau aggregation may be a viable approach for the treatment of AD. NFT consist of hyperphosphorylated tau protein and tau hyperphosphorylation reduces microtubule binding. Several protein kinases are discussed to be involved in tau hyperphosphorylation. We developed novel inhibitors of three protein kinases (gsk-3β, cdk5, and cdk1) and discussed their activity in relation to tau phosphorylation and on tau–tau interaction as a nucleation stage of a tau aggregation in cells. Strongest effects were observed for those inhibitors with effects on all the three kinases with emphasis on gsk-3β in nanomolar ranges.
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15
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Oh-Hashi K, Fujimura K, Norisada J, Hirata Y. Expression analysis and functional characterization of the mouse cysteine-rich with EGF-like domains 2. Sci Rep 2018; 8:12236. [PMID: 30111858 PMCID: PMC6093884 DOI: 10.1038/s41598-018-30362-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 07/29/2018] [Indexed: 01/10/2023] Open
Abstract
We have previously identified a novel endoplasmic reticulum (ER) stress-inducible protein, namely, cysteine-rich with EGF-like domains 2 (CRELD2), which is predominantly regulated by ATF6. However, few studies on intrinsic CRELD2 have been published. In the present study, we elucidated the expression of intrinsic CRELD2 in mouse tissues and ER stress- treated Neuro2a cells. Among nine tissues we tested, CRELD2 protein in the heart and skeletal muscles was negligible. CRELD2 expression in Neuro2a cells was induced at the late phase after treatment with tunicamycin (Tm) compared with rapid induction of growth arrest and DNA damage inducible gene 153 (GADD153). On the other hand, another ER stress inducer, thapsigargin, increased the intrinsic CRELD2 secretion from Neuro2a cells. We furthermore established CRELD2-deficient Neuro2a cells to evaluate their features. In combination with the NanoLuc complementary reporter system, which was designed to detect protein-protein interaction in living cells, CRELD2 interacted with not only CRELD2 itself but also with ER localizing proteins in Neuro2a cells. Finally, we investigated the responsiveness of CRELD2-deficient cells against Tm-treatment and found that CRELD2 deficiency did not affect the expression of genes triggered by three canonical ER stress sensors but rendered Neuro2a cells vulnerable to Tm-stimulation. Taken together, these findings provide the novel molecular features of CRELD2, and its further characterization would give new insights into understanding the ER homeostasis and ER stress-induced cellular dysfunctions.
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Affiliation(s)
- Kentaro Oh-Hashi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
| | - Keito Fujimura
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Junpei Norisada
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Yoko Hirata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.,Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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16
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Norisada J, Fujimura K, Amaya F, Kohno H, Hirata Y, Oh-hashi K. Application of NanoBiT for Monitoring Dimerization of the Null Hong Kong Variant of α-1-Antitrypsin, NHK, in Living Cells. Mol Biotechnol 2018; 60:539-549. [DOI: 10.1007/s12033-018-0092-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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17
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Oh-Hashi K, Furuta E, Fujimura K, Hirata Y. Application of a novel HiBiT peptide tag for monitoring ATF4 protein expression in Neuro2a cells. Biochem Biophys Rep 2017; 12:40-45. [PMID: 28955790 PMCID: PMC5613219 DOI: 10.1016/j.bbrep.2017.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 08/09/2017] [Indexed: 10/31/2022] Open
Abstract
A split NanoLuc assay system consisting of two fragments, large N-terminal and small C-terminal regions (NanoBiT), was developed to investigate protein-protein interactions within living cells. Interestingly, the replacement of five amino acids among 11 C-terminal amino acids dramatically increased affinity against the large N-terminal fragment, LgBiT, and the complex had NanoLuc luciferase activity. In this study, we first applied this small fragment, HiBiT, to elucidate the expression of ATF4 protein by transient overexpression of HiBiT-tagged ATF4. According to the regulation of intrinsic ATF4 protein, stabilization of HiBiT-tagged ATF4 with a proteasome inhibitor, MG132, was observed by detecting luciferase activity in cell lysate and after SDS-PAGE and transfer onto a PVDF membrane. Next, we knocked-in the HiBiT-epitope tag into the ATF4 gene using the CRISPR/Cas9 system and rapidly selected positive clones by measuring luciferase activity in an aliquot of each cell suspension. Using a selected clone, we observed that the expression of HiBiT-tagged ATF4 in the selected cells varied in response to treatment with protein synthesis inhibitors or proteasome inhibitors and tunicamycin. Altogether, this novel HiBiT tag is a useful tool to evaluate the endogenous expression levels of proteins of interest.
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Affiliation(s)
- Kentaro Oh-Hashi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.,Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Eri Furuta
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Keito Fujimura
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yoko Hirata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.,Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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